Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study

Abstract

Aminoacyl-tRNA synthetases (aaRSs), a family of ubiquitous and essential enzymes, can bind target tRNAs and catalyze the aminoacylation reaction in genetic code translation. In this work, we explore the dynamic properties and allosteric communication of human mitochondrial phenylalanyl-tRNA synthetase (hmPheRS) in free and bound states to understand the mechanisms of its tRNA Phe recognition and allostery using molecular dynamics simulations combined with the torsional mutual information-based network model. Our results reveal that hmPheRS's residue mobility and inter-residue motional coupling are significantly enhanced by tRNA Phe binding, and there occurs a strong allosteric communication which is critical for the aminoacylation reaction, suggesting the vital role of tRNA Phe binding in the enzyme's function. The identified signaling pathways mainly make the connections between the anticodon binding domain (ABD) and catalytic domain (CAD), as well as within the CAD composed of many functional fragments and active sites, revealing the co-regulation role of them to act coordinately and achieve hmPheRS's aminoacylation function. Besides, several key residues along the communication pathways are identified to be involved in mediating the coordinated coupling between anticodon recognition at the ABD and activation process at the CAD, showing their pivotal role in the allosteric network, which are well consistent with the experimental observation. This study sheds light on the allosteric communication mechanism in hmPheRS and can provide important information for the structure-based drug design targeting aaRSs.

Study of the Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase by Transfer Entropy via an Improved Gaussian Network Model and Co-evolution Analyses

“…For the N-terminus and bottom structural fragment, RNA binding makes them change from an entropy source to a primary sink, which receives a large amount of information from some other functional regions. The results are consistent with our previous findings that the N-terminus in the tRNA-bound state receives information from the ABD, and the bottom structural fragment significantly enhances the motion coupling between the ABD and CAD, promoting the aminoacylation reaction upon RNA binding . The ABD plays a role of an entropy source in a more steady and whole way in the tRNA-bound state, which is consistent with the role of tRNA binding in aminoacylation activation.…”

“…Figure A makes it clear that the ABD is the entropy donor (allosterically driving region) and the CAD functions as the entropy acceptor (allosterically driven region), which is consistent with the ABD’s functions in anticodon recognition and information transmission to the CAD to achieve hmPheRS’s catalytic activation . Meanwhile, the ABD has a relatively high flexibility (Figure S2), which is important for it to control the tRNA anticodon recognition, and modulate the allosteric coupling within the system for maintaining hmPheRS’s aminoacylation activity . Additionally, the functional regions in CAD can also be distinguished well.…”

“…The corresponding function annotations are listed in Table . Experiments found that certain mutations in hmPheRS’s anticodon binding domain (ABD) can significantly affect the catalytic efficiency of its active sites in the catalytic domain (CAD), although the two sites are separated by ≤80 Å. , Structural studies, including ours, suggest the conformational flexibility of the functional regions and the long-range allosteric couplings between the domains are essential for hmPheRS’s aminoacylation activity. , With regard to allostery, recent findings show it is entropic in nature and depends on the information transfer between two sites through residues’ coordinated fluctuations . Currently, the molecular mechanism by which the long-range allosteric information transfers between ABD and CAD is not completely clear.…”

“…In particular, the N-terminal region, which is in contact with tRNA in the aminoacylation reaction and plays a key role in signal transmission, is shown to be a strong entropy sink or acceptor (Figure D). For the bottom structural fragment, the characteristic region of hmPheRS is vital for enhancing long-range allosteric coupling of CAD with ABD, , and its entropy-accepting behavior is also well highlighted (Figure D). Thus, dfcfGNM MD can clearly distinguish the allosterically driving and driven regions.…”

“…Bhattacharyya et al investigated the signal transmission pathways in pyrrolysyl-tRNA synthetase by weighing the network based on the noncovalent interactions extracted from MD trajectories . Our group built the weighted network based on the residue torsion angle mutual information obtained from MD trajectories to investigate the allosteric communication in hmPheRS . All of these network-based methods can highlight the key residues and allosteric pathways in proteins, but they are not enough to reveal the direction information about allosteric pathways due to their not considering the causality in intramolecular couplings.…”